+
Open data
-
Basic information
Entry | Database: PDB / ID: 2rb1 | ||||||
---|---|---|---|---|---|---|---|
Title | 2-ethoxyphenol in complex with T4 lysozyme L99A | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / protein cavities | ||||||
Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Graves, A.P. / Boyce, S.E. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Rescoring docking hit lists for model cavity sites: predictions and experimental testing Authors: Graves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / Shoichet, B.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rayC ![]() 2razC ![]() 2rb0C ![]() 2rb2C ![]() 2rbnC ![]() 2rboC ![]() 2rbpC ![]() 2rbqC ![]() 2rbrC ![]() 2rbsC ![]() 2rbtC ![]() 2rbuC ![]() 2rbvC ![]() 2rbwC ![]() 2rbxC ![]() 2rbyC ![]() 2rbzC ![]() 2rc0C ![]() 2rc1C ![]() 2rc2C ![]() 184lS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18359.023 Da / Num. of mol.: 1 / Mutation: L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→52.41 Å / Num. all: 29774 / Num. obs: 29774 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.004 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.632 / Num. unique all: 2936 / Χ2: 1.007 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 184L Resolution: 1.7→52.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.885 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.094 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→52.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|